On 11/01/2011 12:21 PM, Andrew Voronkov wrote: > I don t knwo whether it is possible to parametrize ligand and > optimize its position using simulated annealing and loop rmodeling, > so kind of imitating induced fit. Has anyone tried this and question > to Modeller Caretaker - is it potentially possible?
You can certainly treat ligands flexibly if you want, but you will need to obtain topology and force field information for them: http://salilab.org/modeller/9.10/FAQ.html#8
Loop modeling uses a statistical potential that is derived from a database of known (PDB) protein structures. It does not contain protein-ligand interactions. So you will also have to add your own interaction terms to simulate the binding between the ligand and the loop.
Ben Webb, Modeller Caretaker